Publication Information (EuropePMC) | |
Title | A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease. |
PubMed ID | 37414900(Europe PMC) |
doi | 10.1038/s41591-023-02429-x |
Publication Date | July 6, 2023 |
Journal | Nat Med |
Author(s) | Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV. |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS003725 (GPS_Mult) |
PGP000466 | Patel AP et al. Nat Med (2023) |
Coronary artery disease | coronary artery disease | 1,296,172 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003725/ScoringFiles/PGS003725.txt.gz | |
PGS003726 (GPS_CADANC) |
PGP000466 | Patel AP et al. Nat Med (2023) |
Coronary artery disease | coronary artery disease | 1,296,172 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003726/ScoringFiles/PGS003726.txt.gz | |
PGS003727 (GPS_CADEUR) |
PGP000466 | Patel AP et al. Nat Med (2023) |
Coronary artery disease | coronary artery disease | 1,125,113 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003727/ScoringFiles/PGS003727.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score |
PGS Sample Set ID (PSS) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
Classification Metrics | Other Metrics | Covariates Included in the Model |
PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|---|
PPM018420 | PGS003725 (GPS_Mult) |
PSS010961| African Ancestry| 7,281 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.25 [1.07, 1.46] OR: 1.39 [1.17, 1.67] |
— | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018421 | PGS003725 (GPS_Mult) |
PSS010962| East Asian Ancestry| 1,464 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.72 [1.13, 2.6] OR: 2.14 [1.34, 3.49] |
— | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018419 | PGS003725 (GPS_Mult) |
PSS010960| European Ancestry| 308,264 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.75 [1.71, 1.78] OR: 2.14 [2.1, 2.19] |
— | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018422 | PGS003725 (GPS_Mult) |
PSS010963| South Asian Ancestry| 8,982 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.62 [1.49, 1.77] OR: 2.02 [1.83, 2.23] |
— | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018423 | PGS003725 (GPS_Mult) |
PSS010964| African Ancestry| 33,096 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | OR: 1.25 [1.21, 1.29] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018424 | PGS003725 (GPS_Mult) |
PSS010965| European Ancestry| 124,467 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | OR: 1.72 [1.69, 1.75] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018425 | PGS003725 (GPS_Mult) |
PSS010966| Hispanic or Latin American Ancestry| 16,433 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | OR: 1.61 [1.53, 1.7] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018426 | PGS003725 (GPS_Mult) |
PSS010967| South Asian Ancestry| 16,874 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | OR: 1.83 [1.69, 1.99] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018427 | PGS003726 (GPS_CADANC) |
PSS010960| European Ancestry| 308,264 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.73 [1.69, 1.76] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018428 | PGS003726 (GPS_CADANC) |
PSS010961| African Ancestry| 7,281 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.18 [1.01, 1.37] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018430 | PGS003726 (GPS_CADANC) |
PSS010963| South Asian Ancestry| 8,982 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.6 [1.47, 1.74] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018431 | PGS003727 (GPS_CADEUR) |
PSS010960| European Ancestry| 308,264 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.67 [1.64, 1.7] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018432 | PGS003727 (GPS_CADEUR) |
PSS010961| African Ancestry| 7,281 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.15 [0.99, 1.34] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018433 | PGS003727 (GPS_CADEUR) |
PSS010962| East Asian Ancestry| 1,464 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.54 [1.03, 2.32] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018434 | PGS003727 (GPS_CADEUR) |
PSS010963| South Asian Ancestry| 8,982 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.57 [1.44, 1.7] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PPM018429 | PGS003726 (GPS_CADANC) |
PSS010962| East Asian Ancestry| 1,464 individuals |
PGP000466 | Patel AP et al. Nat Med (2023) |
Reported Trait: Coronary artery disease | HR: 1.64 [1.09, 2.48] | — | — | age, sex and the first ten principal components of genetic ancestry | — |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
PSS010960 | ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 | Mean = 12.0 years Range = [11.2, 12.7] years |
[ ,
45.6 % Male samples |
Mean = 57.3 years | European | — | UKB | Excluding first released tranche of genotypes from UKBB |
PSS010961 | ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 | Mean = 12.0 years Range = [11.2, 12.7] years |
[ ,
43.5 % Male samples |
Mean = 52.4 years | African unspecified | — | UKB | — |
PSS010962 | ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 | Mean = 12.0 years Range = [11.2, 12.7] years |
[ ,
37.2 % Male samples |
Mean = 53.0 years | East Asian | — | UKB | — |
PSS010963 | ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 | Mean = 12.0 years Range = [11.2, 12.7] years |
[ ,
54.1 % Male samples |
Mean = 53.8 years | South Asian | — | UKB | — |
PSS010964 | ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 | — | [
|
— | African American or Afro-Caribbean | — | MVP | Excluding individuals in published GWAS (GCST90132302) |
PSS010965 | ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 | — | [
|
— | European | — | MVP | Excluding individuals in published GWAS (GCST90132302) |
PSS010966 | ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 | — | [
|
— | Hispanic or Latin American | — | MVP | Excluding individuals in published GWAS (GCST90132302) |
PSS010967 | ICD10: I21.X, I22.X, I23.X, I24.1, or I25.2; K40.1-40.4, K41.1-41.4, K45.1-45.5, K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, or K75.8-75.9 ICD9: 410.X, 411.0, 412.X, or 429.79 | — | [
|
— | South Asian (Bangladeshi, Pakistani) |
— | G&H | Excluding individuals in published GWAS (GCST90140952) |